FMO DATABASE

FMODB ID: 98ZR2

Calculation Name: 5XE2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XE2

Chain ID: A

ChEMBL ID:

UniProt ID: P9WII5

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-792067.772686
FMO2-HF: Nuclear repulsion	750884.352874
FMO2-HF: Total energy	-41183.419812
FMO2-MP2: Total energy	-41302.912045

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:GLU)

Summations of interaction energy for fragment #1(A:1:GLU)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-53.39	-50.039	10.769	-7.185	-6.935	0.072

Interaction energy analysis for fragmet #1(A:1:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.869 / q_NPA : -0.939

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	MET	0	-0.058	-0.016	1.836	-34.776	-32.755	10.022	-6.654	-5.389	0.070
4	A	4	ASN	0	0.040	0.034	3.032	13.075	14.171	0.749	-0.507	-1.338	0.002
5	A	5	ALA	0	0.004	-0.005	4.472	-4.038	-3.908	-0.001	-0.019	-0.111	0.000
6	A	6	PRO	0	0.005	0.031	6.162	-3.071	-3.071	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.037	-0.038	9.675	-0.305	-0.305	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.800	0.871	12.588	-16.989	-16.989	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.002	-0.010	16.111	-0.255	-0.255	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.006	0.016	12.366	0.799	0.799	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.013	-0.015	16.903	-0.313	-0.313	0.000	0.000	0.000	0.000
12	A	12	TYR	0	0.016	-0.013	11.636	1.236	1.236	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.841	0.905	17.331	-15.704	-15.704	0.000	0.000	0.000	0.000
14	A	14	CYS	0	-0.008	0.011	17.696	1.422	1.422	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.838	-0.936	19.398	12.228	12.228	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.051	0.042	19.587	0.538	0.538	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.023	0.014	22.937	-0.485	-0.485	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.112	-0.067	25.937	-0.514	-0.514	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.044	0.034	26.185	-0.485	-0.485	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.058	-0.031	23.596	0.125	0.125	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.881	0.940	23.383	-11.918	-11.918	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.010	0.005	21.661	0.701	0.701	0.000	0.000	0.000	0.000
23	A	23	TRP	0	0.034	0.009	19.296	-0.671	-0.671	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.026	-0.004	19.156	0.700	0.700	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.029	0.025	13.953	-0.587	-0.587	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.002	-0.015	17.189	-0.486	-0.486	0.000	0.000	0.000	0.000
27	A	27	SER	0	0.014	0.015	14.765	-0.876	-0.876	0.000	0.000	0.000	0.000
28	A	28	ASN	0	0.018	0.004	15.083	1.668	1.668	0.000	0.000	0.000	0.000
29	A	29	ASN	0	0.124	0.044	11.377	1.048	1.048	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.029	0.010	10.328	2.477	2.477	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.864	0.908	10.634	-18.757	-18.757	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.039	0.040	10.696	0.637	0.637	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.929	0.970	4.656	-34.073	-33.969	-0.001	-0.005	-0.097	0.000
34	A	34	HIS	0	0.010	-0.002	6.433	4.155	4.155	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.014	-0.007	8.371	-2.301	-2.301	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.062	0.012	8.843	3.449	3.449	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.820	-0.886	10.504	21.557	21.557	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.035	-0.015	11.641	1.365	1.365	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.004	0.008	14.272	-1.181	-1.181	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.017	0.001	17.656	0.604	0.604	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.008	0.001	19.508	-0.764	-0.764	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.952	0.997	22.604	-11.029	-11.029	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.004	-0.005	23.236	-0.437	-0.437	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.033	-0.028	26.259	-0.100	-0.100	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.041	0.009	29.681	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.053	-0.017	32.764	-0.189	-0.189	0.000	0.000	0.000	0.000
47	A	47	ARG	1	1.019	1.012	34.415	-7.976	-7.976	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.893	0.959	35.233	-9.149	-9.149	0.000	0.000	0.000	0.000
49	A	49	THR	0	-0.021	-0.018	36.754	0.133	0.133	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.003	0.007	35.671	-0.292	-0.292	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.039	0.010	35.634	0.235	0.235	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.007	-0.010	31.900	0.128	0.128	0.000	0.000	0.000	0.000
53	A	53	TRP	0	-0.119	-0.074	31.054	0.340	0.340	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.004	-0.001	29.191	-0.279	-0.279	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.012	0.005	30.234	0.277	0.277	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.005	0.007	24.891	0.122	0.122	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.004	-0.008	29.889	-0.467	-0.467	0.000	0.000	0.000	0.000
58	A	58	PRO	0	0.025	0.006	30.470	0.307	0.307	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.077	-0.051	28.650	-0.187	-0.187	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.702	-0.782	25.777	12.519	12.519	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.011	0.005	21.715	-0.413	-0.413	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.004	0.001	22.641	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	63	THR	0	0.006	0.001	26.530	-0.326	-0.326	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.015	-0.001	29.021	0.265	0.265	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.019	-0.028	30.533	-0.208	-0.208	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.036	0.017	25.338	0.221	0.221	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.003	-0.010	27.482	-0.555	-0.555	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.038	0.008	27.150	0.363	0.363	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.767	-0.851	28.228	9.835	9.835	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.135	-0.069	26.774	-0.071	-0.071	0.000	0.000	0.000	0.000
71	A	71	ILE	0	0.024	0.002	22.844	0.502	0.502	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.842	-0.901	22.355	12.598	12.598	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.062	-0.055	17.502	0.576	0.576	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.033	0.029	16.596	-0.551	-0.551	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.034	0.012	13.965	1.263	1.263	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.768	0.866	6.070	-43.186	-43.186	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.918	-0.961	10.920	24.217	24.217	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.832	-0.910	12.942	16.194	16.194	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.092	-0.046	10.917	-1.056	-1.056	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.050	0.026	14.091	0.685	0.685	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.878	-0.934	14.557	18.063	18.063	0.000	0.000	0.000	0.000
82	A	82	TYR	0	-0.028	-0.023	13.745	-0.947	-0.947	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.065	-0.039	15.823	-0.947	-0.947	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.030	0.014	17.860	-0.968	-0.968	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.832	-0.900	15.417	21.627	21.627	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.052	-0.028	19.324	-0.962	-0.962	0.000	0.000	0.000	0.000
87	A	87	THR	0	-0.008	-0.024	21.960	0.185	0.185	0.000	0.000	0.000	0.000
88	A	88	PRO	0	0.047	0.002	22.522	-0.127	-0.127	0.000	0.000	0.000	0.000
89	A	89	ALA	0	-0.006	0.012	24.515	-0.246	-0.246	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.013	-0.049	26.651	-0.441	-0.441	0.000	0.000	0.000	0.000
91	A	91	MET	0	0.044	0.032	20.553	-0.125	-0.125	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.015	0.000	24.794	0.098	0.098	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.853	0.932	27.392	-10.912	-10.912	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.044	0.014	24.184	-0.220	-0.220	0.000	0.000	0.000	0.000
95	A	95	ASN	0	0.007	0.012	23.979	0.543	0.543	0.000	0.000	0.000	0.000
96	A	96	THR	0	0.000	0.007	26.577	-0.163	-0.163	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.003	0.015	28.983	-0.212	-0.212	0.000	0.000	0.000	0.000
98	A	98	LEU	0	0.001	-0.012	23.501	-0.117	-0.117	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.008	0.010	27.768	-0.071	-0.071	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.027	-0.021	29.881	-0.365	-0.365	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.022	-0.019	29.476	-0.259	-0.259	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.059	-0.022	25.922	-0.037	-0.037	0.000	0.000	0.000	0.000
103	A	103	GLY	0	-0.010	0.004	30.643	-0.093	-0.093	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.027	-0.004	28.256	-0.123	-0.123	0.000	0.000	0.000	0.000
105	A	105	PRO	0	-0.015	-0.001	32.965	-0.173	-0.173	0.000	0.000	0.000	0.000
106	A	106	TRP	0	-0.042	-0.040	29.213	0.052	0.052	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.020	0.022	32.149	0.047	0.047	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:GLU)